Chewbbaca update

[nilchia]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

This update resolves two issues:

1. chewBBACA AlleleCall checks the file extensions. So it does not recognize a FASTA file in the history without an extension.
2. ExtractCgMLST works fine with a normal chewBBACA pipeline but if the user gets the allele profiles from another package or wants to analyze the joined_profile results, there would be a problem because it only takes AlleleCall output. With this update, the user can define the inputs manually.

[bgruening]

Do we need the element identifier here? Or can we just name it input/foo.fa

[nilchia]

AlleleCall accepts multiple input FASTAs. I think in that case it overwrites the inputs. Am I right?

[bgruening]

You can use foo_1 foo_2 please search in this repo for enumerate ... We do that often

[nilchia]

Cool!
I did it with:

        #for i,file in enumerate($input_file)
        ln -sf '$file' 'input/fasta_${i}.${file.ext}' &&
        #end for

One thing, the result of AlleleCall is a tabular file with row names corresponding to the FASTA file names.
So the result would be something like:

rather than:

[bgruening]

yeah, thats bad. Ok lets keep the element_identifier then, but please sanatize them as here for example:

tools-iuc/tools/picard/picard_macros.xml

Line 33 in 1056d5c

#set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))